I have etched my name into a finished blade and cleaned it up after the fact but usually I will finish the blade to the last grit of hand sanding and etch it in, then after the neutralizing of the etchant, I will go over it again with the final grit size. I do this whether it is carbon or Damascus.

I used to do the logo as the last step before final sharpening, but you run the risk of the etch going badly after you already have the knife together. You can clean up a dirty etch on a finished knife, but it's tougher. Consequently, the last dozen or so I have etched the logo after the final polishing but before handle assembly. If you get a little bit of fuzzy on your etch, you can use a hard backing and sandpaper one grit finer than your final polish. It takes off the fuzz without messing up your blade finish. Still important to make full clean strokes.

I always (repeat Always) etch my mark before final assembly. I also hand sand the ricasso one step finer than the blade. So if my blade is finished to 400, then the ricasso goes to 600 and so on. The mark base will always be 600 or finer. I find that the coarser the finish, the more likely you will wind up with a fuzzy mark. Using a good quality stencil also helps make a crisp etch, much more so than the etcher itself. Almost any etcher will work, but the stencil quality is critical. I have tried to put the mark on some knives after the handle is attached, but getting it centered is always a hassle as is keeping the etch from attacking the guard or bolster.After etch and neutralizing, I go back over the mark with 600 or finer paper to remove any stray marks or blemishes caused by errant etching solution.